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What is structural resolution?
Resolution is a measure of the quality of the data that has been collected on the crystal containing the protein or nucleic acid. ... Lower resolution structures, with resolution of 3 Å or higher, show only the basic contours of the protein chain, and the atomic structure must be inferred.
What is b factor in crystallography?
B-factor: “temperature-factor” or “Debye-Waller factor.” A factor that can be applied to the X-ray scattering term for each atom (or for groups of atoms) that describes the degree to which the electron density is spread out.
What is the meaning of Resolution in crystallography?
Resolution. Resolution is a measure of the quality of the data that has been collected on the crystal containing the protein or nucleic acid. ... Most crystallographic-defined structures of proteins fall in between these two extremes.
What is an electron density map?
Electron density maps are the end results of an X-ray structure determination. The maps combine the structural model and the experimentally collected data to represent how well the model fits the data. ... These two maps are then used to correct the model when possible.
What is r free?
Free R (also called Free) “is generally considered the most useful global measure of model-to-data agreement”. It is a statistical quantity introduced in 1992 by Axel T. Bringer to assess the quality of a model from X-ray crystallographic data.
What is occupancy in PDB file?
The primary information stored in the PDB archive consists of coordinate files for biological molecules. These files list the atoms in each protein, and their 3D location in space. These files are available in several formats (PDB, MACIF, XML).
How do I view a PDB file?
Since these files are plain text, you can open the PDB file in a text editor too. Palm Desktop should be able to open PDB files that are in the Palm Database file format, but you might have to first rename it to have the . PRC file extension for that program to recognize it. To open a Palm DOC PDB file, try SDU Viewer.
What is in PDB file?
Program database (PDB) is a proprietary file format (developed by Microsoft) for storing debugging information about a program (or, commonly, program modules such as a DLL or EXE). PDB files commonly have a .PDB extension. A PDB file is typically created from source files during compilation.
What are atomic coordinates?
Atomic coordinate files are the data files that specify three-dimensional (3D) molecular structures. At a minimum, they must specify the positions of each atom in space, typically with X, Y and Z Cartesian coordinates, and the chemical element each atom represents.
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